Variation, of course, is only one part of the recipe for evolutionary change. In order to shift average characteristics of a population over time, natural selection needs to be acting on that variation.
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Evolution Basics: Natural Selection and the Human Lineage, Part 2

April 19, 2013Tags:Genetics, History of Life

Today's entry was written by
Dennis Venema.
You can read more about what we believe here.

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we examine how natural selection is acting on an aspect of human biology in the present day.

In yesterday’s post, we described some of the early steps on the path to the present-day human amylase gene cluster, and the role that natural selection played in the process. Having set the stage, we’re now ready to continue the story—and, as we’ll see, it was a long and winding path from this starting point to arrive at what we see in the present day.

As you will recall, the early evolutionary steps in this process (a) duplicated the original human pancreatic amylase gene, and (b) later changed the activity of one of the copies, such that it was no longer made in the pancreas, but rather in saliva. We further noted that this new variant (which we can abbreviate as “1 pancreas / 1 salivary”) came under selection and replaced the “2 pancreas / 0 salivary” variant that it arose from. Having arrived at this point our ancestors would have had amylase enzyme secreted into the small intestine by the pancreas, but also a new function, amylase secretion from the parotid gland into saliva. This salivary amylase would have provided an advantage in an environment with access to starchy foods, since amylase can break down more starch into glucose with enzymes made in both locations than it can with merely two copies made in the pancreas.

This was not the end of the story, however: the stage was now set for further mutational steps that would also be selected for.

What happens next is more straightforward duplication events, similar to the duplication events we have seen before. This time, however, the duplication copies the newer salivary amylase gene. This duplication results in yet another new variant (1 pancreas / 2 salivary) that is selected for as well, since it is an improvement over the (1 pancreas / 1 salivary) variant it arose from. Later on, there is another duplication that spans both salivary copies to give a combination of 1 pancreas / 4 salivary copies. At this point there are five distinct gene copies, all side by side in the genome, and this variant also replaces the previous version due to selection.

The next stage, however, has a twist. Recall that it was the insertion of a retroviral DNA sequence that originally converted the second amylase gene copy from a pancreas enzyme to a salivary enzyme. This retrovirus sequence was copied along with the rest of this gene when it was duplicated, and at this point is still present in each of the four salivary gene copies. Later, the retrovirus excises itself from one of the four salivary copies (leaving only a small “footprint” behind), reverting it back to production in the pancreas. This results in a new (2 pancreas / 3 salivary) variant. This new variant also comes under selection and replaces the (1 pancreas +4 salivary) variant that it arose from, since the doubling of the pancreas enzyme offers an advantage at this point, even if it comes at the expense of one of the salivary genes. The salivary copy that was converted back to a pancreatic gene retains a “scar” of once having been a salivary gene—with a genetic “there-and-back again” tale to tell.

If this all seems a little convoluted, I don’t blame you—it is convoluted. But that is the point—this is the convoluted history that is written into this region of our genomes. It ably demonstrates that we have been shaped by mutation and natural selection. These are the very same types of mutation and selection events that scientists have observed in real time in experimental organisms, and they demonstrate that random mutation (again, random in the biological sense, as we discussed yesterday) is quite capable of producing new genes with new properties, and that natural selection is able to shift a population over to new, advantageous variants that arise.

And on it goes, even to this day

At this point you might think that the story was over, and that all humans now have the “2 pancreas / 3 salivary” version of the amylase gene cluster. What is interesting is that this is not actually the case. Some humans have even more copies of the salivary amylase genes – individuals with up to a staggering 10 salivary copies side-by-side have been identified. At the other end of the scale, some humans have less than the “standard” 3 copies, perhaps just two or even only one. These variants arose as deletions from the “standard” 2 pancreas / 3 salivary arrangement. In other words, humans are hugely variable for the number of salivary amylase genes – as a population, we are not uniform. Some of us have more amylase in our saliva than others.

Variation, of course, is only one part of the recipe for evolutionary change. In order to shift average characteristics of a population over time, natural selection needs to be acting on that variation. To test the hypothesis that natural selection is acting on human salivary amylase copy number variation, researchers have looked to see if human populations using a high starch diet have different copy numbers, on average, than human populations using a diet low in starch.

The results are striking, and support the hypothesis that natural selection is acting on copy number variation in modern humans. In populations that have historically used a high starch diet, the average salivary amylase copy number is significantly higher than for populations that historically use a low starch diet. Detailed molecular analysis of the genomic region containing the amylase gene cluster in populations using a high-starch diet also showed signs of selection, in that they had greatly reduced variability (as one would expect if selection was acting). This reduced variability was not seen in these same populations for other genome regions with variable copy numbers. Taken together, these results support the hypothesis that natural selection is at work on the amylase gene cluster region in human populations. So, it seems that this story is still unfolding—and that we can observe a snapshot of the process at our moment in history.

Completing the circle: from man to dog

Two further lessons we can draw from this example require us to think back to the similar process that occurred during dog domestication. In dogs, there are numerous copies of pancreatic amylase genes, and dogs are currently variable for the number of copies they have. These duplication events in the dog lineage owe their selective advantage to the prior amylase duplication events in the human lineage. The human duplications were part of improving our reproductive success as we shifted over to a diet with greater starch content. While humans made the shift, dog populations associated with humans experienced a similar shift in environment—they, too, had access to greater amounts of starch.

This altered environment provided a selective advantage to variants within the dog population that, like their human companions, could benefit from increased starch consumption. The shift in the first species (humans) has a direct link to the shift in a second species (dog). This is an example of what is known as co-evolution: where two species in close contact act as major features of the other species’ environment, and selective changes in the one species shift what is advantageous for the other species. This human / dog amylase story is also an example of evolution “repeating” itself in two independent lineages—in this case, similar gene duplication events that boosted the amount of pancreatic amylase independently in dogs and humans. The technical term for this is convergent evolution—evolutionary paths that arrive independently at the same “solution” in two lineages.

While we will look at co-evolution and convergent evolution in more detail in later posts, it is worth noting these features now, while this example is fresh in our minds. The take-home message here is simple: evolution is not just a chance-based process, but also one that is, at least to a certain degree, repeatable. In part, this repeatability is based on organisms encountering similar environments, and these environments selecting for similar outcomes in both species. In the case of species in close contact, a shift in one species can open up a new opportunity for the second species.

In the next post in this series, we’ll examine further details of how genetic variation arises in populations, and how selection may or may not act on it.

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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lancelot10 - #78759

April 19th 2013

Adaptation of pre existing genome to environmental changes is not proof of evolution.

Surely this adaptation of existing genes to environmental factors such as diet is to be expected. Why is it deemed to be evolution evidence. We have all heard the phrase ” I got used to it ” - this could be diet changes , cold , heat , manual labour etc. This would involve adaptive changes already provided for in our genome. The extra amylase machinery would be what we would expect from a body designed by God. The triggering factors would be the body detecting more carbs in our food. I dont see how this can be classed as evolution - information was not added to the genome but was there already - whether in the DNA , ERV’s or Junk DNA etc.

I knew a farm dog that was fed oats and was healthy - it did not evolve this ability but already had it designed into its genome.

My blond hair gradually changed to black after about 7 years of age - this would be black haired genes taking over for some reason. The African races are dark skinned due to similar changes you have mentioned - but we nearly all have the ability to producemore or less melanin - it is adaptation.

It is tenuous to suggest evolution proof in all of the above especially when there is no mechanism for evolution. None of the above will lead to another species - the dogs wont turn into humans no matter how long they live together. Cave fish can lose their eyesight but get it back again if bred in the light - all due to gene changes - but they are still fish.

If we start at the mythical single cell - how could DNA information be added to it in order to speciate - as I said Darwins tree is upside down - the trunk would need enormous amounts of DNA to branch out into millions of different species.

melanogaster - #78833

April 20th 2013

”If we start at the mythical single cell “

Why would we start at a single cell? Is there any scientific abiogenesis hypothesis in which life starts out as cellular?

lancelot10 - #78843

April 21st 2013

melanogaster.

Yes - your own theory of evolution is based on it. Using your evolutionary logic if all the living is made up of single cells joined in harmony together, which it is , then this means according to evolutionary logic we all must be descended from that single cell.

Darwins theory is based on this fantasy - so the hypothesis should have a mechanism to show how this happened. No science has ever demonstrated this event happens now or in the past - so evolution does not even have a cogent starting point.

Since science should be based on verifiable evidence and there is none the theory should remain rejected.

melanogaster - #78855

April 21st 2013

“Yes - your own theory of evolution is based on it.”

No, evolution is about how living things change, and there are well-tested theories about the mechanisms. Abiogenesis has mere hypotheses. What system of Christian morality advocates putting words in the mouths of other people when you clearly don’t know what you are talking about?

I’ll ask you a simple question again: is there any scientific abiogenesis hypothesis in which life starts out as cellular?

That’s not evolution, that’s an abiogenesis hypothesis. Cite a real one instead of simply making things up, OK?

beaglelady - #78858

April 21st 2013

Guess what? I’m under fire because I don’t believe that God designed the first cell!

Eddie - #78869

April 21st 2013

No, beaglelady; you are under fire because you won’t commit to the view that God designed anything, yet identify yourself as a Christian.

But I don’t want to hijack this thread, which is about natural selection, not the origin of life or God and design; people interested in the discussion you’ve referred to can go to:

Sorry for the interruption; just wanted to provide that link. Back to natural selection!

beaglelady - #78870

April 21st 2013

baloney! I said that God brought forth the universe. And you said that you would spit on the TE God.

Eddie - #78875

April 21st 2013

beaglelady:

Your misrepresentation of my statement, by quoting half of a conditional sentence out of context, is evidently deliberate, given that I already pointed out this misrepresentation on the other thread. And deliberate misrepresentation by out-of-context quoting is a form of academic dishonesty. I ask you politely to desist from this practice.

“Brought forth” does not mean “designed.” Something can be “brought forth” in an unplanned way. You were given a dozen opportunities on the other thread to articulate which facets of the universe and life were, in your view, designed. You simply would not say whether anything was in your view designed, and your general principles, derivable from a number of your remarks, suggested that you thought nothing was. And regarding the first cells, you specifically indicated that you did not believe they were designed. Further, when I several times, in various ways, stated the conclusion I have just given, your answer was silence; you did not contradict me, saying: “No, I in fact believe that X and Y and Z were designed.” So as far as I can tell, my statement above was correct: you have not committed to the view that God designed anything.

If you object to my characterization of your views, please go back to the other thread, where I have asked you about them in multiple postings with a proper, contextualizing discussion. You can attach your complaints and/or your clarifications to any one of my queries; I will find them. And I will certainly retract or modify any statement which is demonstrably a misrepresentation of your words. I am not interested in winning a purely verbal victory. If I agree with what you mean to say, I will acknowledge it.

I won’t comment further on this thread. I don’t want to spoil Dennis’s column by arguing with you over a matter that belongs on another thread. I hope you will take the same attitude.

beaglelady - #78876

April 21st 2013

I’m not going to use the word design. It’s a loaded word, and I don’t want anything to do wtih the ID movement. And I don’t see how God can bring forth the universe in an unplanned way. What does that mean?

As for your conditions for spitting on the TE God, I don’t think we should ever speak of spitting on someone’s god under any condition. I wouldn’t spit on Indian gods, even though they are not real.

Eddie - #78880

April 21st 2013

My answers are in the appropriate place. You know where to look.

beaglelady - #78898

April 22nd 2013

You aren’t going to tell me where to post, and I won’t let you put words in my mouth.

lancelot10 - #78856

April 21st 2013

The theory of evolution is based on the single living cell springing miraculously into existence in a primordial soup of sea water. This is where Darwin’s hypothesis starts - he even tried to draw this cell. Every living thing is supposed to come from this cell which amazingly created its own DNA by sheer chance - are you proposing another hypothesis of evolution - if you are can you please enlighten us all.

“… is based on the single living cell springing miraculously into existence in a primordial soup of sea water.”

No, that’s a falsehood. Biogenesis hypotheses do not go from nothing replicating to cells in one step.

Merv - #78859

April 21st 2013

lancelot10, it may help to clear up lots of ‘category confusion’ between you and others here in your use of the term: evolution. I’m pretty sure from having read your other posts that when you speak of ‘evolution’ what you really mean is what others familiar with these issues carefully distinguish as ‘Evolutionism’. The capitalized ‘-ism’ term can refer to the whole philosophy of naturalism that extends far beyond anything science does or even can support, but nevertheless gets lumped together with the more modest and merely scientific theory of evolution (where the real science is). Since you don’t distinguish between the science and the wider philosophy so often lumped with it—you see no difference and use one term for everything. But be aware that others here do distinguish, and can see confusion in your own approach then that you maybe can’t yet recognize.

So ‘evolution’ (at least the kind that actually has scientific ‘teeth’ or evidence to it) does not include abiogenesis topics with the attendant speculations about how the first self-replicating molecules and their simpler pre-cursors to the presently functioning DNA could have emerged from the organic soup. I’m not suggesting that all such speculation in whatever current form it is in must be wrong—just that the science on that is nowhere close to being ‘filled in’, let alone conclusive, but it becomes much more solid on events after multi-cellular organisms were around.

You mentioned that Darwin’s ‘tree of life’ should really be inverted. Actually, what you seem to advocate with your understanding of Genesis would not be a ‘tree’ at all (inverted or otherwise) but something more like a field of grass. Sure—some stems may split off into several different blades (e.g. like the speciation of dogs), but you essentially see every ‘kind’ as its own special creation from the beginning, right? There would be no ‘trunk’ involved anywhere in your model. Hope the clarifications help.

-Merv

lancelot10 - #78860

April 21st 2013

Merv - I dont see any difference in evolution or evolutionism - what about science and scientism or sport and sportism?

I dont believe in Darwin’s or anyone else’s tree of life but was critisising its logic - the trunk holding enough DNA for every species.

Dont agree with your assumptions since evolutionists believe it all started with one cell miraculously coming together - try googling - the first living cell - and you will see what I mean.

If a theory cannot explain its origin then it is not a theory which should be accepted as complete - especially since even the jump from multicellular to say the first fish cannot be explained either. Are we going to start a theory half way down the line by saying dont know what happened in the first two billion years but this is my guess for the last two.

If you are now saying in your field of grass theory that lots of different cells started in many different pools of seawater then this is infinitely less possible than that of one single cell defeating probability science and any attempt to replicate this supposed one off event.

No self replicating molecules or their precursors have been seen - no molecule has replicated itself - we are dealing with fantasy - only God can create all that is seen and unseen.

Yes I believe every living kind was instantly created and has enough DNA to speciate to a lesser or greater degree and this is what we see - one kind does not change into another.

Two major planks of evolution is the single cell and the 5 billion years supposed age of the sediments. Since we see dinos and many other land animals at the bottom of the sediments and fish etc at the top it only means one thing - that the long age is nonsense and with carbon and radio dating of the sediments actual scientific proof that they are young.

Lyell admitted that he had dealt a death blow to Moses account by a very subtle method of falsely aging the sediments - he said attacking the torah head on would have led to vilification by a Bible believing christian society at that time where scientists generally accepted that the fossils and sediments were right in line with a catastrophic flood.

Lyell was a deist but went to church as far as I know - he did not like christianity at all.

Merv - #78862

April 21st 2013

From lancelot10:

I dont see any difference in evolution or evolutionism.

My point exactly.

I can see from your other posts, since you already have your mind made up against deep time and even want to insist that Galileo was wrong (despite the fact that the Catholic church itself now agrees with Galileo) that you will probably have trouble finding a common basis with anyone who has read anything at all about these issues. But if you want to try, you would need to start a massive reading program. One of the many places you can tackle to get some much-needed clarity would be Dennis’ post about the basics of scientific ‘theory’ on this very site:

But that is just one among many issues that need addressing in your post, so I’m not sure you’ll be able to glean profit anywhere else on this site. You misunderstood nearly everything in my previous post— I have no “field of grass” theory” but was trying to give you a better analogy for your own approach.

I wish you the best.

-Merv

beaglelady - #78864

April 21st 2013

Are you taking him seriously?

lancelot10 - #78882

April 22nd 2013

Merv - you are right I dont agree with the long timescale since scientifc evidence is against it

Heliocentrism cannot be proved as in the hundreds of expirements to try to demonstrate it.

As far as I know the magisterium has not deleted geocentrism.

It is the theory of evolution which needs clarity and evidence.

Merv - #78868

April 21st 2013

You may be right—this could be Poe’s law in action. But I prefer to err on the side of assuming sincerity. Besides, other visitors may not be as sure and may gain the mistaken impression that such a post prevailed as the ‘best word’—as difficult as that may be to believe.

Lou Jost - #78878

April 21st 2013

You should be congratulated on your patience and tact, Merv.

beaglelady - #78906

April 22nd 2013

It’s a telling commentary on the nature of Evangelicalism when a poe can blend in perfectly with the crowd. Conrad was an obvious poe but BioLogos put up with him forever.

Joriss - #78891

April 22nd 2013

What Lancelot10 means, as far as I can see, is that the way from carnivore to herbivore need not necessarily be a very long one, if even now a dog can eat oats and stay alive and even be healthy. Maybe he has a point?

beaglelady - #78899

April 22nd 2013

Except that dogs are not becoming herbivores—they’re simply exploiting a different food source by being better able to digest it. (btw, A dog fed only oats will not be healthy.) Many carnivores will regularly eat plants—e.g. bears and coyotes like berries. btw, commercial dog food from the supermarket is largely made of corn. And get this: an astonishing percentage of the food that humans eat has corn in some form in it, or was fed corn before going to slaughter. (Read The Omnivore’s Dilemma: A Natural History of Four Meals by Michael Pollan)

lancelot10 - #78892

April 22nd 2013

Isaiah 11:7 indicates that animals will return to being herbivores in the new creation:

The cow and the bear will graze, their young ones will lie down together, and the lion will eat straw like the ox. Isaiah 11:7 msb.to/ Isaiah11:7

Ronnie - #79023

April 24th 2013

Merv

I will disagree, I think there is a devotion to evolution here on Biologos. Of course, that is why this site exists. I agree with Lancelot that evolution is being given way too much credit for things it may have nothing to do with. Worse, evolution is contrary to the plain word of God. I am all to familiar with the arguments that Genesis is only an allegory and should not be taken as literal, but I think that is a mistake. As Christians, we should give Gods word priority, even if it is contrary to what we’ve been taught to believe, including ‘evolution’ (the large scale kind espoused here on Biologos).

Merv - #79047

April 24th 2013

Ronnie, Lancelot thinks that a geocentricism is the true or most accurate cosmology. And this probably stems from what he sees as the truest, plainest reading of Scripture (and then, also, from subsequent evidence that he apparently finds convincing—I trust I’m not misrepresenting you, Lancelot, and that you will jump in to correct this if I am). So Ronnie, do you agree with Lancelot in this? And if not, then I’m curious to hear you explain to him why you are placing your trust in modern science instead of a plain understanding of Scripture. If you do agree with him (on geocentrism), then of course disregard this entire post.

lancelot10 - #79050

April 24th 2013

Merv - the michelson morley experiment tried to prove that the earth was moving through space - it didnt and similar expirements have been retried hundreds of times - so this is science - heliocentrism cannot be proven and if you do a little study quite a few scientists still say geocentrism is the correct system - and perfectly possible. Since you are on a search for the biblical truth you will find that truth is held by a minority if the truth is God’s word - but it will be the truth - so when the bible clearly teaches geocentrism I will believe it .

However if I ran a church I would not force anyone to believe this theoryagainst their will since it would not be a salvation issue for most - but it could be for some if it led them to doubt God’s word - in salvation areas.

Why not look at the latest arguments on geocentrism . For me it is easier to believe that God stopped the sun and the universe than stopped the earth from spinning during Joshua’s battle .

However since you are trying to box God’s power into the rules of science which He created - you dont believe that either event happened - that Joshua made it up - it was a fable - or symbolic in some way - or maybe Joshua was tired and he imagined this.

Merv - #79057

April 25th 2013

As always, this is not about what God can do but about what God did do and continues doing. I’m aware of the workability of geocentric perspectives from different and arbitrarily workable mathematical coordinate systems, though I will admit I haven’t recently visited any geocentrism web sites to stay up on their latest.

If you wish to believe that “the dog wags his tail” and “the tail wags the dog” are two equal statements, neither of which has any greater claim to reflecting reality than the other since both can be used as ‘stationary’ reference points then that is your right. (Actually—you do claim one is closer to actual truth: insisting that the universe must gyrate wildly about the earth to conform to our stationary observations is equivalent to insisting not only that it cannot be the dog wagging the tail, but that a single stationary flea is making the entire tail—not to mention the poor dog gyrate wildly around it.)

I am glad that you would not be dogmatic about such things.

What the Michelson and Morely experiment led to was an abandonment of the concept of a universally referential ether. That paved the way for Einstein’s (and Galileo’s before him) theory of relative motion. But I’m guessing you don’t buy into relativity despite its ample supporting experimental evidence.

Ronnie, how would you fare in Lancelot’s hypothetical and heliocentrically tolerant church? You can consider this rhetorical. I don’t believe in being obnoxious and argumentative, but if I’ve already crossed that line, then I apologize. You no doubt see where I’m leading with it.

Merv - #79086

April 25th 2013

Wow—did we just hyperspace a couple comments back in this exchange? I could have sworn Lancelot and I both had a post or two beyond this one. Did the sun go backward today without my noticing it?

lancelot10 - #79094

April 25th 2013

Merv - this seems to happen a lot - it is irritating

glsi - #79224

April 28th 2013

Any of you science lovers read the Wall St. Journal? There’s an interesting piece today by Matt Ridley, “Did a Bacterial E.T. Bring Life to Earth?”. It seems that Dr.s Alexei Sharov and Richard Gordon (a geneticist and a biologist) have calculated it would have taken at least 10 billion years for the human genome and other life to have evolved to its present form. Their calculation is based on applying Moore’s Law to biological complexity. Their conclusion is that life had to have started evolving on some other planet long before earth ever came into existence. Panspermia again.

I don’t have a link to the WSJ, but here’s one at the Washington Post:

file:///Users/glennsimonsen/Desktop/What if Moore’s Law applied to humans as well? - Innovations - The Washington Post.webarchive

I wonder what the geneticists here will have to say. Choose a different math model that will better fit their beliefs?

To me it’s just confirmation of what appeared obvious all along: that Darwinian mechanisms wouldn’t have nearly enough time to develop the complex life forms found in the Cambrian, let alone the first cell evolving supposedly from…RNA…?

“Is time real, or the ultimate illusion? Most physicists would say the latter, but Lee Smolin challenges this orthodoxy in his new book, “Time Reborn” … [Smolin] argued for the controversial idea that time is real.”

If anyone wants to brave the actual scientific literature and see how regions of the genome are identified as candidates for positively selected regions, look at this paper. You’ll have to go to your local university library unless you have a subscription to Science.